When offline, method 1
I use this method for "light reading," like when I have a lot of articles to read, and not all of them may get into the synthesis stage. In most scientific journal articles the first page nearly always contain the title and abstract. I rip that page off, or just print that first page online, and then make my notes at the back of that page throughout my skimming/reading. When I am done, I put a rating on the front page, and the file it away into the project folder. I like this method because sometimes seeing just the front page can trigger some sort of photo memory, reminding me more about the overall layout of the article.
I'd also recommend printing over the back of the first page with a Cornell note layout. On the narrower vertical side you can write down page number, on the big box key points, and on the lower box overall personal comments. I often photocopy many pages of Cornell note, and the feed them into the paper tray when I want to print the title/abstract pages.
When offline, method 2
When I am reading more seriously, I use this method. You'll need some highlighters, some index cards, and a pen. I use the highlighters for important quote, and then on the index card I wrote down the DOI number, and the page number, and my comments about the highlighted part. For comments, I try to keep them short and I use different symbols to streamline the reading process:'
- ?: for my own questions.
- T: for tasks, representing some references or websites mentioned in the text that I need to check.
- !: for emphasis.
I have been using a freeware Qiqqa (only available for Windows and Android as of now) and I like it very much. After you have imported the PDF files, you can do many cool things with them:
- Search all content (including text) within the PDF
- Tag each article with your customized tag
- Highlight or crop out sections that you feel important
- Attach sticky notes relevant to the section you highlight/crop
- (Very great function!) Create a report that only contains the materials you generated in steps 3 and 4 above. Qiqqa will lay them all out, and attach the article's information in each of the highlighted/cropped/noted parts. I LOVE this function because it can discern which are quotes and which are my own words... eliminating much risk of accidental plagiarism.
- Support multiple libraries, and you can also sync your articles onto their server. They give free user 500 Mb, and users can always top up the libraries with a very small fee.
- Hyperlinked word cloud for each articles to identify key words and specific terms.
- When you have enough articles, you can use their theme mining function to generate a map of their research theme (still kind of under development).
- Generate concept map.
- Superb bibliographic function. It allows users to search for all the bibliographical information through multiple search engines. With Google Scholar (one of the engines), you can even directly import the references in BibTeX format! I cannot contain my happiness about this function.
For a freeware, this is the first one I felt someone finally got it right. Worth a try.